Academic Record
  

• Faculty Scientist; Institute of Bioinformatics and Applied Biotechnology (IBAB), Bangalore. Research Areas: Bioinformatics, Chemo informatics, Biosensors

• Post Doctoral Research Associate. (2005-2007 July):  Center for Bioinformatics, Biology, Jonsson Rowland Science Center, RPI Troy NY - 12180 USA

Research Areas: Bioinformatics, Comp. Biology and Biophysics

• Ph.D. (1999-2004): Indian Institute of Technology, Bombay, Powai-400076 India

Doctoral Thesis: Stereo chemical Effects in Protein Structure Folding and De novo Design. Research Areas: Computational Biology, Biophysics, Molecular modeling, Protein Design.

• Master of Science in Applied Chemistry, 1998. Cochin University of Science and Technology, Kochi, India.

Specialization: Synthetic Polymers, Industrial Catalysis

Research Interests
 

Chemo informatics, Protein and peptide chemistry, De novo protein design, Solid phase peptide synthesis, Spectroscopic and chromatographic methods of characterization, Computational Biology, Molecular modeling, Computer aided molecular design.

Awards and Scholastic Achievements
 

• Innovative Young Biotechnologist Award (IYBA 2007), Dept. of Biotechnology, Ministry of Science and Technology, Govt. of India. (http://dbtindia.nic.in/awardees/awardmain.html)
• Post Doctoral Fellowship funded by National Science Foundation United States, 2005
• Institute Research Fellowship IIT Bombay, 1999
• CSIR-UGC National Eligibility Test, 1999
• Graduate Aptitude test in Engg. (GATE), 1999
• Cochin University Merit Scholarship (1997,1998) by CUSAT for top two students in each discipline

 Professional Affiliations
 

• American Chemical Society
• The International Society for Computational Biology (ISCB)
• Bio-informatics Organization (http://www.bioinformatics.org/)

Publications
 

• Vibin Ramakrishnan; Ranjit Ranbhor and Susheel Durani.  Existence of Specific "Folds" in Polyproline-II Ensembles of an Unfolded Alanine Peptide Detected by Molecular Dynamics.  JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004) 126, 16332-16333.

• Vibin Ramakrishnan; Ranjit Ranbhor and Susheel Durani.  Probing Main Chain Roles in Protein Structure and Folding Stereochemically. A Simulated Annealing Folding Study of Isotactic, Syndiotactic and Heterotactic Polypeptides. BIOPOLYMERS (2005) 78, 96-105.

• Vibin Ramakrishnan; Ranjit Ranbhor; Anil Kumar and Susheel Durani. The link between Sequence and Conformation in Protein Structures appears to be Stereochemically Established.  JOURNAL OF PHYSICAL CHEMISTRY B (2006) 110, 9314-9323.

• Ranjit Ranbhor; Vibin Ramakrishnan; Anil Kumar and Susheel Durani. The Interplay of Sequence and Stereochemistry in defining Conformation in Proteins and Polypeptides.  BIOPOLYMERS (2006) 83, 537-545.

• Vibin Ramakrishnan, Saeed Salem, Saipraveen Srinivasan, Wilfredo Colon, Mohammed Zaki & Christopher Bystroff. GEOFOLD: A Mechanistic Model to Study the Effect of Topology on Protein Unfolding Pathways and Kinetics. 3DSig. STRUCTURAL BIOLOGY & COMPUTATIONAL BIOPHYSICS. (2008) 25-26.

• Anil Kumar; Vibin Ramakrishnan; Ranjit Ranbhor and Susheel Durani. Homochiral Stereochemistry: The Missing Link of Structure to Energetics in Protein Folding Journal of physical chemistry b  (2009)  113 (51), pp 16435–16442

• Aimy Sebastian and Vibin Ramakrishnan. Computational Biology Applications. SCIENCE OF HORTICULTURE. VOL 3. Ed: K V Peter. (NIPA New Delhi) (2010, Book Chapter).  

• Vibin Ramakrishnan; Saeed Salem; Saipraveen Srinivasan, Mohammed Zaki, Suzanne Mathews, Wilfredo Colon and Christopher Bystroff. Developing a detailed mechanistic model for protein unfolding. (2010) Proc. Natl. Acad. Sci. (being processed)

• Aimy Sebastian and Vibin Ramakrishnan. Representing ‘Biophore’ in one dimension; Applications in early phases of drug discovery. Journal of Chem. Inf. Model. Manuscript ID: ci-2009-00145c Submitted.

• Ranjit Ranbhor, Anil Kumar, Abhijit Tendulkar Vibin Ramakrishnan, and Susheel Durani. Automating Protein Design for Chirality in Side Chain Attachment to be the Stereochemical Alphabet. Biopolymers (2010) final review.

Conference Proceedings (Indexed)

• Vibin Ramakrishnan, Ranjit Ranbhor and Susheel Durani. Stereochemical origins of compactness and stability in proteins. A simulated annealing study of poly L and alternating L, D diastereomer variants of Ac-Ala30-NHMe. 48th Annual Meeting of Biophysical Society, Baltimore, Maryland, USA. Biophys. J S. 2004, 86, 621.

• Ranjit Ranbhor, Vibin Ramakrishnan, Anil Kumar, Abhijit Tendulkar and Susheel Durani. Heterochiral Proteins. De novo Design by Stereochemical Control of Folding. The 19th Annual Symposium of Protein Society, USA. 2005. Boston, USA.
  Protein Science S. 2005, 14, 105.

• Anil kumar, Vibin Ramakrishnan, Ranjit Ranbhor; Susheel Durani. “Poly-L stereochemistry and conformational landscapes of protein folding. Explicit solvent MD of Poly-L and Alternating-L,D octa-alanines.” 51st Annual Meeting of Biophysical Society, CA, USA
  Biophys. J. 94: 195. 2008.

• Anil Kumar; Ranjit Ranbhor; Vibin Ramakrishnan; Susheel Durani. “Simulated Dynamics of Blocked Octa-L-alanine Implicates Inter-Peptide Interaction as Possible Speed Barrier in Protein Folding.” The 21st Annual Symposium of Protein Society, USA. Boston, U.S.A. July 21-25, 2007. Protein Science S (2007) 16, 107. 

• Vibin Ramakrishnan; Saeed Salem; Mohammed Zaki and Christopher Bystroff.  Simulation of Protein Folding Pathways and Folding Kinetics using Statistical Mechanical Model. 5th International Conference on Bioinformatics December 18-20, InCoB 2006, New Delhi. 

Conference Proceedings (Non indexed)

• Vibin Ramakrishnan, Ranjit Ranbhor and Susheel Durani. Stereochemical origins of compactness and stability in proteins. A systematic modeling study of poly L and alternating L, D diastereomer variants of Ac-Ala8-NHMe. NCBS Symposium on Molecules, Machines and Networks 2004 National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore.
• Vibin Ramakrishnan, Ranjit Ranbhor, Anil Kumar and Susheel Durani. Seeds of protein folding in polyproline-II ensembles of unfolded polypeptides. The Second Indian Symposium of Protein Society- Protein Structure and Function. 2004. IIT-Bombay.
• Ranjit Ranbhor, Vibin Ramakrishnan, Anil Kumar and Susheel Durani. De novo design of heterotactic mini-protein. The Second Indian Symposium of Protein Society- Protein Structure and Function. 2004 IIT-Bombay.                         
• Anil Kumar, Ranjit Ranbhor, Abhijit Tendulkar, Kirti Patel, Vibin Ramakrishnan and Susheel Durani. De novo Design with Diversification of Molecular Tacticity. Joint International Conference by American Chemical Society and Council of Scientific and Industrial Research. 2006. National Chemical Laboratory, Pune.
• Ranjit Ranbhor, Vibin Ramakrishnan, Anil Kumar and Susheel Durani. The Link between Sequence and Conformation in Protein Structures could be Stereochemically Established. The Eighth Symposium of Chemical Research Society of India. 2006. IIT-Bombay, Mumbai.
• Anil Kumar, Ranjit Ranbhor, Vibin Ramakrishnan and Susheel Durani. Inter-peptide Interaction and Protein Folding Mechanisms: A Molecular Dynamics Study of Blocked Octa-L-Alanine in Explicit Solvent. IITB Symposium Symposium. August 19, 2006. Department of Chemistry, IIT-Bombay, Mumbai.
• Ranjit Ranbhor, Vibin Ramakrishnan, Anil Kumar, Abhijit Tendulkar and Susheel Durani. Computational Design of Heterochiral Protein Assemblies. 75th Annual Meeting, Society of Biological Chemists (India) December 8-11, 2006 at Jawaharlal Nehru University, New Delhi.
• Ranjit Ranbhor, Anil Kumar, Vibin Ramakrishnan, Abhijit Tendulkar and Susheel Durani. Computational Design of Protein Dimers in C2-Symmetry. 5th International Conference on Bioinformatics December 18-20, 2006 at Hotel Ashok, New Delhi.
• Anil Kumar, Vibin Ramakrishnan, Ranjit Ranbhor and Susheel Durani. Inter-peptide Interaction and Protein Folding Mechanism. Molecular Dynamics of Blocked Octa-L-Alanine in Explicit Solvent. 5th International Conference on Bioinformatics December 18-20, 2006 at Hotel Ashok, New Delhi.
• Anil Kumar; Ranjit Ranbhor; Vibin Ramakrishnan; Susheel Durani. “Molecular Dynamics of Blocked Octa-L-alanine Implicates Inter-Peptide Electrostatics as Possible Speed Barrier in Protein Folding.” Indian Biophysical Society-2007 (National Symposium on Biophysics: Trends in Biomedical Research) New Delhi, Feburary 13-15, 2007
• Anil Kumar; Ranjit Ranbhor; Vibin Ramakrishnan; Susheel Durani. “Poly-L Structure and Peptide Dipolar Interaction in Protein Folding Speed and Specificity.” Western Regional Humboldt Kolleg 2007 Jaipur, Rajasthan, September 28-30, 2007.